NanoLC-FT-ICR MS improves proteome coverage attainable for approximately 3000 laser-microdissected breast carcinoma cells

Proteomics assays hold great promise for unraveling molecular events that underlie human diseases. Effective analysis of clinical samples is essential, but this task is considerably complicated by tissue heterogeneity. Laser capture microdissection (LCM) can be used to selectively isolate target cells from their native tissue environment. However, the small number of cells that is typically procured by LCM severely limits proteome coverage and biomarker discovery potential achievable by conventional proteomics platforms. Herein, we describe the use of nanoLC-FT-ICR MS for analyzing protein digests of 3000 LCM-derived tumor cells from breast carcinoma tissue, corresponding to 300 ng of total protein. A total of 2282 peptides were identified by matching LC-MS data to accurate mass and time (AMT) tag databases that were previously established for human breast (cancer) cell lines. One thousand and three unique proteins were confidently identified with two or more peptides. Based on gene ontology categorization, identified proteins appear to cover a wide variety of biological functions and cellular compartments. This work demonstrates that a substantial number of proteins can be detected and identified from limited number of cells using the AMT tag approach, and opens doors for high-throughput in-depth proteomics analysis of clinical samples.     

Novel approaches to analyse glomerular proteins from smallest scale murine and human samples using DIGE saturation labelling

Loss of renal function is often associated with the injury of kidney glomeruli. It is therefore necessary to understand the mechanisms leading to progressive glomerular diseases; this may be addressed using proteomics. Until now, however, analysis of the glomeruli proteome using 2-DE has been technically hampered by low protein yields from scarce samples. To circumvent this problem, we developed a procedure which allows the human and mouse glomeruli proteome to be analysed. In this study, two different approaches were used to isolate mouse and human glomerular protein from kidney cortex. Mouse glomeruli were extracted by embolisation magnetic beads into the glomerular capillaries. Laser capture microdissection (LCM) was utilised to harvest glomeruli from human biopsy material. Human and murine samples were analysed using a fluorescence saturation labelling technique. Using 3 microg mouse glomerular protein a total of 2900 spots were resolved for differential proteome analysis. Moreover, it was also demonstrated for the first time that only ten glomeruli (0.5 microg) picked by LCM from a slide of a human kidney biopsy material were sufficient to visualise 900 spots. This novel strategy paves the way for future experiments aimed at investigating functional proteomics of glomerular diseases in humans and in mice.     

基于荧光标记的怒江流域桔小实蝇（Bactrocera dorsalis）的迁移扩散

2005年7月在云南怒江流域地区,以荧光粉作为标记物,采用“标记-释放-回收”方法,对怒江流域桔小实蝇迁移扩散规律进行了研究。以释放点潞江坝为中心,东南西北4个方位设立桔小实蝇回收点,经过7d的回捕,从释放点沿潞江以北至六库沿线共回收到的标记桔小实蝇43头,最远在距释放点以北97 km 的地方回收到标记桔小实蝇5头。沿怒江在释放点以南,仅在小于29 km 的范围内回收到标记桔小实蝇17头。释放点东面和西面未能回收到标记桔小实蝇。分析释放点以北各回收点标记桔小实蝇与非标记桔小实蝇的相互关系揭示,非标记桔小实蝇与标记桔小实蝇在空间动态中具有相同的行为模式,由此推论非标记桔小实蝇与标记桔小实蝇可能来自同一种群。分析怒江流域区的自然地理发现,潞江坝桔小实蝇可借助怒江两边高大山脉形成的天然河谷通道,在适宜的气候条件下,在北上气流的携带下,实现由南向北的远距离迁移扩散;同时,由于高大山脉的阻隔,使潞江坝桔小实蝇没能向东西两个方向作远距离扩散迁移。研究首次揭示了在特定峡谷地区桔小实蝇扩散迁移现象,为桔小实蝇迁移扩散研究提供了新鲜实例,为在当地制定切实有效的桔小实蝇防治策略提供了基础信息。     

Adverse Effects of Capture and Handling Little Bustard

Abstract Capturing wild animals for research or conservation purposes may cause some adverse effects, which is only acceptable if these are outweighed by conservation benefits. We used information from 3 on-going telemetry studies on the endangered little bustard (Tetrax tetrax) in Western Europe to evaluate the risk factors associated with capture and handling. Of 151 telemetered birds, 23 (15.2%) exhibited impaired mobility and coordination after release, probably related to the occurrence of capture myopathy. Among the 23 impaired birds, 10 (43.5%) died before recovering normal mobility (6.6% of all birds captured). Logistic regression analyses identified longer handling time, longer restraint time, use of cannon nets, and capture of juveniles as inducing factors for these disorders. We conclude that little bustard is fairly susceptible to suffering ataxia and paresia after release as a result of restraint associated with capture and manipulation. Researchers can reduce this risk by keeping handling and restraint time below 10–20 minutes, particularly when using cannon nets or when capturing juveniles.     

Forests do not limit bumble bee foraging movements in a montane meadow complex

1. Understanding the roles of habitat fragmentation and resource availability in shaping animal movement are integral for promoting species persistence and conservation. For insects such as bumble bees, their movement patterns affect the survival and reproductive potential of their colonies, as well as the pollen flow of plant species. However, the understanding of their mobility or the impact of putative barriers in natural environments is limited due to the technical difficulties of studying wild populations. 2. Genetic mark–recapture was used to estimate the foraging distance, resource use, and site connectivity of two bumble bee species in a montane meadow complex composed of open meadows within a matrix of forest. 3. There was no evidence that forests or changes in landcover function as barriers to the fine-scale movement for either species. Substantially greater colony-specific foraging distances were found for Bombus vosnesenskii (maximum: 1867 m) compared to Bombus bifarius (maximum: 362 m). Despite this difference in absolute range, both species were detected across putative forest barriers at frequencies expected by uninhibited movement. Siblings separated by greater distances were more likely to be foraging on different floral species, potentially suggesting a resource-based motivation for movement. 4. These results suggest that bumble bee foraging patterns are influenced by species-specific differences in movement capacity, with little influence of matrix composition between resource patches. They also support the perspective that habitat conservation for bumble bees should prioritise providing abundant and diverse patches of resources within species-specific movement radii with less emphasis on matrix composition.     

The Probable Mechanism for Silicon Capture by Diatom Algae: Assimilation of Polycarbonic Acids with Diatoms—Is Endocytosis a Key Stage in Building of Siliceous Frustules?

Many organisms including unicellular (diatoms, radiolaria, and chrysophytes), higher plants (rice and horsetail) and animals (sponges) use silica as a main part of skeletons. The bioavailable form of silicon is silicic acid and the mechanism of silicic acid penetration into living cells is still an enigma. Macropinocytosis was assumed as a key stage of the silicon capture by diatoms but assimilation of monomeric silicic acid by this way requires enormous amounts of water to be passed through the cell. We hypothesized that silicon can be captured by diatoms via endocytosis in the form of partially condensed silicic acid (oligosilicates) whose formation on the diatom surface was supposed. Oligosilicates are negatively charged nanoparticles and similar to coils of poly(acrylic acid) (PAA). We have synthesized fluorescent tagged PAA as well as several neutral and positively charged polymers. Cultivation of the diatom Ulnaria ferefusiformis in the presence of these polymers showed that only PAA is able to penetrate into siliceous frustules. The presence of PAA in the frustules was confirmed with chromatography and PAA causes various aberrations of the valve morphology. Growth of U. ferefusiformis and two other diatoms in the presence of tri- and tetracarbonic fluorescent tagged acids points to the ability of diatoms to recognize substances that bear four acidic groups and to include them into siliceous frustules. Thus, partial condensation of silicic acid is a plausible first stage of silicon assimilation.     

Comparison of Two Techniques for Surveying Headwater Stream Amphibians

Abstract: We compared rubble-rousing versus light-touch stream amphibian survey techniques in multiple 1-m plots across 10 streams in southwest Washington, USA. Specifically, we wanted to determine if light-touch surveys provide unbiased estimates of abundance (i.e., provide counts correlated with rubble-rousing counts) and which method would provide more cost-effective presence or absence information. Rubble-rousing, a common technique for surveying stream-associated amphibians in the Pacific Northwest, took 12 times as long as light-touch to apply. Abundance estimates and standard errors for rubble-rousing were consistently higher than those for light-touch for all life stages for the coastal tailed frog (Ascaphus truei) and Columbia torrent salamander (Rhyacotriton kezeri). Except for eggs, light-touch detected all life stages found during rubble-rousing. For frogs, only some rubble-rousing abundance estimates, mostly involving second-year larvae, were highly correlated with their light-touch counterparts, whereas for salamanders, similar comparisons generated high correlations across most life stages. Correlations between methods were consistently greater for salamanders than for frogs. However the smaller tailed frog sample sizes and the cryptozoic nature of some life stages may have contributed to this pattern. Depending on the degree to which researchers can tolerate false-negative error rates, light-touch may prove less costly than rubble-rousing for detecting species presence. For the cost of obtaining one rubble-rousing sample, many light-touch samples can be used across a range of habitats for detecting species patchily distributed.     

Thermal Imaging to Study Stress Non-invasively in Unrestrained Birds

Stress, a central concept in biology, describes a suite of emergency responses to challenges. Among other responses, stress leads to a change in blood flow that results in a net influx of blood to key organs and an increase in core temperature. This stress-induced hyperthermia is used to assess stress. However, measuring core temperature is invasive. As blood flow is redirected to the core, the periphery of the body can cool. This paper describes a protocol where peripheral body temperature is measured non-invasively in wild blue tits (Cyanistes caeruleus) using infrared thermography. In the field we created a set-up bringing the birds to an ideal position in front of the camera by using a baited box. The camera takes a short thermal video recording of the undisturbed bird before applying a mild stressor (closing the box and therefore capturing the bird), and the bird’s response to being trapped is recorded. The bare skin of the eye-region is the warmest area in the image. This allows an automated extraction of the maximum eye-region temperature from each image frame, followed by further steps of manual data filtering removing the most common sources of errors (motion blur, blinking). This protocol provides a time series of eye-region temperature with a fine temporal resolution that allows us to study the dynamics of the stress response non-invasively. Further work needs to demonstrate the usefulness of the method to assess stress, for instance to investigate whether eye-region temperature response is proportional to the strength of the stressor. If this can be confirmed, it will provide a valuable alternative method of stress assessment in animals and will be useful to a wide range of researchers from ecologists, conservation biologists, physiologists to animal welfare researchers.